Age | Commit message (Collapse) | Author | Files | Lines | |
---|---|---|---|---|---|
2023-08-04 | Mesotrione data and vignette | Johannes Ranke | 1 | -27/+27 | |
The vignette illustrates pH dependent degradation (covariate modelling) with some detail for the parent compound. Also, a bug in the saem method of the illparms function was fixed, which prevented to find ill-defined parameters in cases where e.g. slopes of covariate models have a negative estimate. | |||||
2023-05-19 | Prepare release of v1.2.4v1.2.4 | Johannes Ranke | 1 | -12/+12 | |
- Update DESCRIPTION - Update Makefile to document how to use R-patched - Remove markup from two URLs to avoid CRAN NOTE - Switch two vignettes from html_document to html_vignette to save space in the docs directory, also avoiding a CRAN NOTE - Complete rebuild of pkgdown docs for release | |||||
2023-04-16 | Skip the Eigenvalue based saem test | Johannes Ranke | 1 | -8/+12 | |
It took too long, and this solution method is not recommended. We are saving 140 seconds here on my system, so more time is saved on travis. | |||||
2023-04-15 | Increase test coverage | Johannes Ranke | 1 | -15/+15 | |
Also, using mkin analytical solutions for more than one observed variable is not supported (but could be if out_values would be reordered). | |||||
2023-04-15 | Make predefined symbols safer | Johannes Ranke | 1 | -14/+15 | |
We still need to create a parallel processing cluster _after_ creating a compiled model that is moved to a user defined location, at least I did not find another way to make it work. This is not a problem with parallel processing without a cluster, which is not available on Windows. | |||||
2023-04-06 | Fix a bug with moved DLLs and current deSolve | Johannes Ranke | 1 | -12/+12 | |
In mkinmod, dll_info was not included in the returned model object in the case that the DLL was moved to a user defined directory. This is now fixed. | |||||
2023-04-02 | Deal with covariates in summary for saem.mmkin objects | Johannes Ranke | 1 | -13/+13 | |
2023-04-01 | Update tests on 5950x | Johannes Ranke | 1 | -29/+29 | |
Update platform dependent test plots | |||||
2023-03-23 | Support covariates in endpoints() | Johannes Ranke | 1 | -18/+17 | |
2023-03-22 | Fix typo in mkinerrmin | Johannes Ranke | 1 | -26/+27 | |
Thanks to Sebastian Meyer for spotting it. | |||||
2023-02-17 | Finish adapting to upcoming deSolve | Johannes Ranke | 1 | -13/+13 | |
2022-12-15 | List random effects correlations in output if any | Johannes Ranke | 1 | -10/+10 | |
Update docs | |||||
2022-12-12 | Run tests with new CPU and RAM | Johannes Ranke | 1 | -26/+26 | |
2022-12-07 | Check slopes in saemix covariate models | Johannes Ranke | 1 | -25/+16 | |
2022-12-06 | Some parplot improvements | Johannes Ranke | 1 | -16/+25 | |
llquant argument, improved legend text, tests | |||||
2022-12-02 | Avoid error message at testthat termination | Johannes Ranke | 1 | -24/+23 | |
https://github.com/r-lib/processx/issues/236 | |||||
2022-12-01 | Possibility to manually specify no_random_effects in mhmkin | Johannes Ranke | 1 | -24/+24 | |
2022-11-29 | Complete starting values in summary for saem.mmkin fits | Johannes Ranke | 1 | -17/+17 | |
Also update tests to the changes in mhmkin (see NEWS) | |||||
2022-11-19 | Confirm which test fail on R-develv1.2.1 | Johannes Ranke | 1 | -16/+16 | |
2022-11-18 | Move two saem fits from setup script to skipped tests | Johannes Ranke | 1 | -22/+22 | |
Save winbuilder/CRAN check time... | |||||
2022-11-18 | Use cluster with two cores to reduce windows check time | Johannes Ranke | 1 | -18/+19 | |
2022-11-18 | Make mixed model test data permanent to ensure reproducibility | Johannes Ranke | 1 | -14/+14 | |
To ensure that tests on different platforms work on the same data, the mixed modelling test data previosly generated in tests/testthat/setup_script.R were generated once using the script in inst/dataset/generation/ds_mixed.R, and are now distributed with the package. | |||||
2022-11-18 | Round parameters with signif() before printing | Johannes Ranke | 1 | -10/+10 | |
This will hopefully make the test pass on all relevant platforms. | |||||
2022-11-18 | Pass error.init to saemix_model, show in parplot | Johannes Ranke | 1 | -19/+19 | |
Due to an oversight, error.init was not really passed to saemix_model in saem.mmkin. The new initial values were reverted to c(1, 1), in order to avoid changing the test results. Initial values for error model parameters are now shown in parplot.multistart. | |||||
2022-11-16 | Update DESCRIPTION and NEWS, check and test | Johannes Ranke | 1 | -18/+18 | |
2022-11-16 | Address platform dependence that surfaced on winbuilder | Johannes Ranke | 1 | -23/+23 | |
2022-11-15 | Import saemix for easier profiling, update online docs | Johannes Ranke | 1 | -8/+8 | |
2022-11-14 | Automatic starting parameters for saem.mmkin | Johannes Ranke | 1 | -16/+16 | |
For the case of mkin transformations. This gives faster convergence, and appears to avoid problems with numeric ODE solutions | |||||
2022-11-08 | Show DFOP g equivalent of SFORB in summary, test | Johannes Ranke | 1 | -13/+13 | |
2022-11-08 | Simplify SFORB also in the endpoint function | Johannes Ranke | 1 | -13/+13 | |
2022-11-08 | Simplify SFORB analytical solution, whitespace | Johannes Ranke | 1 | -20/+20 | |
I do not know why the formulae for b1 and b2 on page 64 of FOCUS kinetics (2014) were not simplified. Clearly, the term k12 * k21 - (k12 + k1output) * k21) can be simplified to - k1output * k21 The test for equivalence of DFOP and SFORB fits verifies that the change is OK. I also removed trailing whitespaces, substituted tab characters by two whitespaces and removed indenting of text in paragraphs describing parameters in roxygen comments to unify formatting. | |||||
2022-11-04 | Attempt at automatic setting of random effects | Johannes Ranke | 1 | -19/+19 | |
Based on parameters in the separate fits that fail the t-test. | |||||
2022-11-01 | Fix plotting saem fits with covariates | Johannes Ranke | 1 | -9/+9 | |
2022-11-01 | Fix illparms tests | Johannes Ranke | 1 | -45/+12 | |
2022-11-01 | Improved printing for illparms() | Johannes Ranke | 1 | -14/+47 | |
For the case of single fits and no ill-defined parameters found | |||||
2022-10-31 | Fix R CMD check | Johannes Ranke | 1 | -10/+10 | |
2022-10-29 | Another attempt to make the test robust | Johannes Ranke | 1 | -18/+18 | |
As the last update failed on travis. Now we should be more robust, as rounding to one digit works better when parameters are log-transformed (mkin transformations) in the output. | |||||
2022-10-28 | Rename parhist to parplot and make it generic | Johannes Ranke | 1 | -21/+21 | |
That parhist name was not the brightest idea, as it does not show histograms. | |||||
2022-10-28 | Export status method for mhmkin, move to status.R | Johannes Ranke | 1 | -20/+20 | |
2022-10-28 | Update test to renamed method | Johannes Ranke | 1 | -13/+13 | |
2022-10-26 | Really test anova output, test covariates | Johannes Ranke | 1 | -11/+11 | |
2022-10-26 | Reduced sfo model for multistart.saem.mkin tests | Johannes Ranke | 1 | -13/+13 | |
2022-10-26 | Remove kernel density estimate from llhist | Johannes Ranke | 1 | -15/+15 | |
2022-10-26 | Try to make multistart (more) reproducible | Johannes Ranke | 1 | -9/+9 | |
2022-10-26 | Tests pass locally | Johannes Ranke | 1 | -21/+19 | |
2022-10-26 | Make multistart work with testthat scopes | Johannes Ranke | 1 | -12/+20 | |
Also skip long-running test with saem using the analytical from mkin | |||||
2022-10-25 | Change DFOP mixed model data in tests, updates | Johannes Ranke | 1 | -12/+12 | |
2022-10-25 | Complete documentation and fix a bug | Johannes Ranke | 1 | -11/+11 | |
The bug was introduced by the changes in summary.saem.mmkin.R and surfaced in the tests when using saemix transformations. | |||||
2022-10-17 | SFORB in saem, update for mhmkin and multistart | Johannes Ranke | 1 | -8/+8 | |
2022-10-14 | Select best fit from multistart, use in parhist | Johannes Ranke | 1 | -13/+13 | |
- Add 'best' and 'which.best' generics with methods for multistart objects - Per default, scale the parameters in parhist plots using the fit with the highest log likelihood. |